Hello, I am trying to study particular atoms in a molecule. I am giving an input babel sdf (attached to this post) of one molecule into the python script posted below and am trying to look at indices and atomic masses of the atoms I am interested in. I have noticed that, after calling mol.make3D(), properties of the particular atoms I am studying, such as atomic mass and index number, become messed up. Does anyone know why this is the case? I have posted an example output from running this script with the given sdf below. Thanks!
*Script:*
import pybel
from sys import argv
mols = [x for x in pybel.readfile('sdf', 'interesting_atom.sdf')]
for mol in mols:
interesting_atoms = []
interesting_atom_indices = list(set(mol.data['PRIMARY_SOM'].split()))
for index in interesting_atom_indices:
interesting_atoms.append(mol.OBMol.GetAtomById(int(index)))
print map(lambda x: x.GetIndex(), interesting_atoms)
print map(lambda x: x.GetAtomicMass(), interesting_atoms)
mol.make3D()
mol.localopt()
print map(lambda x: x.GetIndex(), interesting_atoms)
print map(lambda x: x.GetAtomicMass(), interesting_atoms)
Output:
[1, 15, 29] -- initial indices of interesting atoms
[12.0107, 12.0107, 1.00794] -- atomic masses of these interesting atoms
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 3 stereocenter(s) in this molecule (RXNREGNO#97673
MTB12598)
with Atom Ids as follows: 11 17 19
[0, 4133926103, 0] -- new indices
[114.818, 0.0, 1.00794] -- new atomic masses
interesting_molecule.sdf
Description: Binary data
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